5T37 | pdb_00005t37

crystal structure of mPGES-1 bound to inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5T37/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2016-08-24 Released: 2017-03-01 
• Deposition Author(s): Luz, J.G., Antonysamy, S., Partridge, K., Fisher, M.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Discovery and characterization of [(cyclopentyl)ethyl]benzoic acid inhibitors of microsomal prostaglandin E synthase-1.

Partridge, K.M., Antonysamy, S., Bhattachar, S.N., Chandrasekhar, S., Fisher, M.J., Fretland, A., Gooding, K., Harvey, A., Hughes, N.E., Kuklish, S.L., Luz, J.G., Manninen, P.R., McGee, J.E., Mudra, D.R., Navarro, A., Norman, B.H., Quimby, S.J., Schiffler, M.A., Sloan, A.V., Warshawsky, A.M., Weller, J.M., York, J.S., Yu, X.P.

(2017) Bioorg Med Chem Lett 27: 1478-1483

• PubMed: 28190634 
• DOI: https://doi.org/10.1016/j.bmcl.2016.11.011
• Primary Citation Related Structures: 
  5T36, 5T37, 5TL9


• PubMed Abstract: 
  

  We describe a novel class of acidic mPGES-1 inhibitors with nanomolar enzymatic and human whole blood (HWB) potency. Rational design in conjunction with structure-based design led initially to the identification of anthranilic acid 5, an mPGES-1 inhibitor with micromolar HWB potency. Structural modifications of 5 improved HWB potency by over 1000×, reduced CYP2C9 single point inhibition, and improved rat clearance, which led to the selection of [(cyclopentyl)ethyl]benzoic acid compound 16 for clinical studies. Compound 16 showed an IC ₈₀ of 24nM for inhibition of PGE ₂ formation in vitro in LPS-stimulated HWB. A single oral dose resulted in plasma concentrations of 16 that exceeded its HWB IC ₈₀ in both rat (5mg/kg) and dog (3mg/kg) for over twelve hours.

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Organizational Affiliation: 
• Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA. Electronic address: [e-mail].
Eli Lilly Biotechnology Center, San Diego, CA 92121, USA.
Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA.
Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA; Retired.
Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA; Present/Permanent address: Discovery Sciences, Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.12 kDa 
• Atom Count: 1,438 
• Modeled Residue Count: 148 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin E synthase	A	154	Homo sapiens	Mutation(s): 0  Gene Names: PTGES, MGST1L1, MPGES1, PGES, PIG12 EC: 5.3.99.3 (PDB Primary Data), 1.11.1 (UniProt), 2.5.1.18 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O14684 (Homo sapiens) Explore O14684  Go to UniProtKB:  O14684
PHAROS:  O14684 GTEx:  ENSG00000148344

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
758	B [auth A]	2-chloro-5-{[(2,2-dimethylpropanoyl)amino]methyl}-N-(1H-imidazol-2-yl)benzamide C16 H19 Cl N4 O2 MBAHGUNQNAJTLD-UHFFFAOYSA-N
GSH	C [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
BOG	D [auth A], E [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4	F [auth A], G [auth A], H [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
758	BindingDB:  5T37	IC50: min: 240, max: 870 (nM) from 6 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	C [auth A]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.24	α = 90
b = 76.24	β = 90
c = 124.098	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Luz, J.G., Antonysamy, S., Partridge, K., Fisher, M.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-03-15
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-03-06
  Changes: Data collection, Database references, Structure summary